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The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

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  • Wei Huang
  • Joohyun Kim
  • Shantenu Jha
  • Fareed Aboul-ela

Abstract

Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. To link ligand/aptamer binding to conformational switching, we constructed models of an S-adenosyl methionine (SAM)-I riboswitch RNA segment incorporating elements of the expression platform, allowing formation of an antiterminator (AT) helix. Using Anton, a computer specially developed for long timescale Molecular Dynamics (MD), we simulated an extended (three microseconds) MD trajectory with SAM bound to a modeled riboswitch RNA segment. Remarkably, we observed a strand migration, converting three base pairs from an antiterminator (AT) helix, characteristic of the transcription ON state, to a P1 helix, characteristic of the OFF state. This conformational switching towards the OFF state is observed only in the presence of SAM. Among seven extended trajectories with three starting structures, the presence of SAM enhances the trend towards the OFF state for two out of three starting structures tested. Our simulation provides a visual demonstration of how a small molecule (

Suggested Citation

  • Wei Huang & Joohyun Kim & Shantenu Jha & Fareed Aboul-ela, 2013. "The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch," PLOS Computational Biology, Public Library of Science, vol. 9(5), pages 1-13, May.
    • Handle: RePEc:plo:pcbi00:1003069
    DOI: 10.1371/journal.pcbi.1003069
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    References listed on IDEAS

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    1. Rebecca K. Montange & Robert T. Batey, 2006. "Structure of the S-adenosylmethionine riboswitch regulatory mRNA element," Nature, Nature, vol. 441(7097), pages 1172-1175, June.
    2. Marc Parisien & François Major, 2008. "The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data," Nature, Nature, vol. 452(7183), pages 51-55, March.
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